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The need for common standards in the field of proteomics, to allow the transfer and public domain deposition of proteomic data, is now widely recognized. The Proteomics Standards Initiative (PSI) sponsored by the Human Proteome Organization (HUPO) has been actively developing such standards, which are now entering the implementation stage and are being adopted by data users, data producers (both hardware and software manufacturers) and bench scientists. The PSI has already published XML data interchange standards in the field of mole-cular interactions (PSI-MI), and a stable XML schema has now been established to handle mass spectro-metry (MS) data (mzData). During the course of the Spring HUPO-PSI Workshop, these existing standards were significantly advanced whilst progress was also made in an exchange format to enable transfer of MS analytical data (mzIdent) and gel electrophoresis (GE) data. These activities are a part of the encompassing General Proteomics Standard (GPS), which is now producing a working object model (PSI-OM) and producing ontologies, which, in many cases, will be shared by many applications and have wider usage than the field of proteomics alone.
The University of Siena and the Italian Human Proteomics Organization hosted the Second HUPO-PSI workshop in April 2005. The theme of this workshop was very much that of advancing the current standards to increase flexibility whilst maintaining stability and, at the same time, pushing forward the newer areas to ensure that these standards enter the implementation phase as quickly as possible. Similar to previous workshops [1], parallel sessions worked on the established areas of molecular interactions (MI) and MS whilst the GPS group tackled both the Minimal Information About a Proteomics Experiment (MIAPE) documentation and initiated a new track with discussions on the establishment of XML standards to capture and transfer GE. The three groups shared a common session where the establishment of a single ontology to describe protein modifications was discussed; previous meetings with the US National Instititutes of Health (NIH) had identified this as a shared requirement across the entire field of proteomics.
General Proteomics Standard
A number of MIAPE documents are in various stages of completion; the parent document and three technology-specific modules for MS, MS informatics and GE, which has been split into GE and GE informatics. The MS docu-ment has...